1 Introduction

2 Setting up the data

The allen data set contains expression values for 379 cells from the mouse visual cortex [@tasic2016adult], and can be loaded directly by calling ReprocessedAllenData() and specifying the value for the assays parameter. To begin with, we assign the output of this call to an sce object and inspect it.

2.1 Load an example data set - 1k Brain cells

Throughout this vignette, you’ll use the 1k Brain Cells dataset from 10xgenomics.com which contains expression values for 1301 brain cells from an E18 mouse. It ships with singlecellutils and is already preprocessed as a SingleCellExperiment data object from the SingleCellExperiment package. We can inspect the dataset with:

data("neuron_1k_v3", package = "singlecellutils")
neuron_1k_v3
#> class: SingleCellExperiment 
#> dim: 31053 1301 
#> metadata(0):
#> assays(1): umi
#> rownames(31053): ENSMUSG00000051951 ENSMUSG00000089699 ...
#>   ENSMUSG00000096730 ENSMUSG00000095742
#> rowData names(10): gene_id gene_name ... total_umi log10_total_umi
#> colnames(1301): AAACGAATCAAAGCCT-1 AAACGCTGTAATGTGA-1 ...
#>   TTTGGTTAGTAATCCC-1 TTTGTTGGTATGGAAT-1
#> colData names(9): is_cell_control total_features_by_umi ...
#>   pct_umi_in_top_200_features pct_umi_in_top_500_features
#> reducedDimNames(0):
#> spikeNames(0):

Creating a single cell RNA-Seq report with i2dash.scrnaseq

26 August 2019

Package

1 Introduction

2 Setting up the data

2.1 Load an example data set - 1k Brain cells